Progressing adaptation of SARS-CoV-2 to humans

2021

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Background. COVID-19 has spread worldwide since it appeared in 2019. In contrast to many other countries with epidemics, Japan differed in that it avoided lockdowns and instead asked people for self-restraint. A travel campaign was conducted with a huge budget, but the number of PCR tests is severely limited. These choices may have influenced the course of the epidemic. Methods. The increase or decrease in the classes of SARS-CoV-2 variants was estimated by analyzing the published sequences with an objective multivariate analysis. This methodology does not rely on unverifiable assumptions. It observes the samples in multiple directions, digesting complex differences into simpler forms. The results were compared over time with the number of confirmed cases, PCR tests, and overseas visitors. Results. Three epidemic peaks in Japan have been caused by domestically mutated variants. However, due to the relaxation of immigration restrictions, several infective variants have been imported from abroad and are currently competing for expansion. In other countries, there are few other cases where multiple variants have peaked. The chaotic situation in Japan will continue for a while, in part, because no effort has been made to find asymptomatic carriers and details of the vaccination program are undecided.

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…The conditions for finding variants from each country are as follows (Konishi 2021): (original axes)…”

Section: Methodsmentioning

confidence: 99%

“…The worldwide COVID-19 pandemic continues (WHO 2020), with rapid mutation of variants (Konishi 2021). In Japan, the epidemic began with spread from a cruise ship.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Effect of control measures on the pattern of COVID-19 Epidemics in Japan

2021

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SARS-CoV-2 mutations among minks show reduced lethality and infectivity to humans

2020

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SARS-CoV-2 infection in minks has become a serious problem, as the virus may mutate and reinfect humans; some countries have decided to cull minks. Here, the virus sequencing data in minks were analysed and compared to those of human-virus. Although the mink-virus maintained the characteristics of human-virus, some variants rapidly mutated, adapting to minks. Some mink-derived variants infected humans, which accounted for 40% of the total SARS-CoV-2 cases in the Netherlands. These variants appear to be less lethal and infective compared to those in humans. Variants that have mutated further among minks were not found in humans. Such mink-viruses might be suitable for vaccination for humans, such as in the case of the smallpox virus, which is less infective and toxic to humans.

COVID-19 epidemics monitored through the logarithmic growth rate and SIR model

2021

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Background: The SIR model is often used to analyse and forecast the expansion of an epidemic. In this model, the number of patients exponentially increases and decreases, resulting in two phases. Therefore, in these phases, the logarithm of infectious patients changes at a constant rate, the logarithmic growth rate K. However, in the case of the coronavirus disease 2019 (COVID19) epidemic, K never remains constant but increases and decreases linearly; therefore, the SIR model does not fit that seen in reality. We would like to clarify the cause of this phenomenon and predict the occurrence of COVID19 epidemics. Methods: We simulated a situation in which smaller epidemics were repeated with short time intervals. The results were compared with the epidemic data from 279 countries and regions. Results: In the simulations, the K values increased and decreased linearly, similar to the real data. Because the previous peak covered the initial increase in the epidemic, K did not increase as much as expected; rather, the difference in the basic reproduction number R0 appeared in the slope of increasing K. Additionally, the mean infectious time τ appeared in the negative peaks of K. By using the R0 and τ estimated from the changes in K, changes in the number of patients could be approximated using the SIR model. This supports the appropriateness of the model for evaluating COVID-19 epidemics. By using the model, the distributions of the parameters were identified. On average, an epidemic started every eleven days in a country. The worldwide mean R0 was 2.9; however, this value showed an exponential character and could thus increase explosively. In addition, the average τ was 12 days; this is not the native value but represents a shortened period because of the isolation of patients. As τ represents the half-life, the infectious time varies among patients; hence, prior testing should be performed before isolation is lifted. The changes in K represented the state of epidemics and were several weeks to a month ahead of the changes in the number of confirmed cases. In the actual data, when K was positive on consecutive days, the number of patients increased a few weeks later. In addition, if the negative peaks of K could not be reduced to as small as 0.1, the number of patients remained high. Thus, the number of K-positive days and mean infectious time had a clear correlation with the total number of patients. In such cases, mortality, which was lognormally distributed, with a mean of 1.7%, increased. To control the epidemic, it is important to observe K daily, not to allow K to remain positive continuously, and to terminate a peak with a series of K-negative days. To do this, it was necessary to shorten τ by finding and isolating a patient earlier. The effectiveness of the countermeasures is apparent in τ. The effect of vaccination, in terms of controlling the epidemic, was limited.